Starting phenix.real_space_refine on Wed Feb 14 02:30:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9a_35263/02_2024/8i9a_35263.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9a_35263/02_2024/8i9a_35263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9a_35263/02_2024/8i9a_35263.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9a_35263/02_2024/8i9a_35263.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9a_35263/02_2024/8i9a_35263.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9a_35263/02_2024/8i9a_35263.pdb" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 51 5.16 5 C 5353 2.51 5 N 1458 2.21 5 O 1547 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 16": "OD1" <-> "OD2" Residue "A ASP 49": "OD1" <-> "OD2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A ASP 381": "OD1" <-> "OD2" Residue "B ASP 38": "OD1" <-> "OD2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 163": "OD1" <-> "OD2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B ASP 205": "OD1" <-> "OD2" Residue "B ASP 267": "OD1" <-> "OD2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "B ASP 333": "OD1" <-> "OD2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8409 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1858 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain breaks: 3 Chain: "B" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2415 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 103 Chain: "G" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 400 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1658 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "C" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2006 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 14, 'TRANS': 257} Chain breaks: 2 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 75 Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1, 'PEPT-D': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 5.15, per 1000 atoms: 0.61 Number of scatterers: 8409 At special positions: 0 Unit cell: (84.64, 119.6, 122.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 51 16.00 O 1547 8.00 N 1458 7.00 C 5353 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.03 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 172 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.55 Conformation dependent library (CDL) restraints added in 1.8 seconds 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL D 9 " Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 39.0% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 15 through 40 removed outlier: 3.539A pdb=" N ALA A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 265 through 279 removed outlier: 3.516A pdb=" N ASN A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 removed outlier: 4.141A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.595A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.792A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.534A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 56 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 220 through 224 Processing helix chain 'C' and resid 20 through 50 Proline residue: C 39 - end of helix removed outlier: 3.545A pdb=" N VAL C 44 " --> pdb=" O GLY C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 74 removed outlier: 3.519A pdb=" N TRP C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE C 61 " --> pdb=" O ASN C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 85 removed outlier: 4.201A pdb=" N SER C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 126 Proline residue: C 99 - end of helix removed outlier: 3.687A pdb=" N ASN C 105 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 134 Processing helix chain 'C' and resid 135 through 161 Proline residue: C 156 - end of helix Processing helix chain 'C' and resid 332 through 345 Processing helix chain 'C' and resid 345 through 363 removed outlier: 3.550A pdb=" N VAL C 360 " --> pdb=" O TYR C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 403 Proline residue: C 392 - end of helix removed outlier: 3.659A pdb=" N LEU C 401 " --> pdb=" O GLY C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 435 removed outlier: 3.924A pdb=" N HIS C 418 " --> pdb=" O MET C 414 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N CYS C 429 " --> pdb=" O SER C 425 " (cutoff:3.500A) Proline residue: C 432 - end of helix Processing helix chain 'C' and resid 439 through 450 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.822A pdb=" N ASP A 223 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N PHE A 222 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.755A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.531A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.949A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.674A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.679A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.737A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.924A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.005A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.670A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 140 through 141 removed outlier: 3.877A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 146 through 149 removed outlier: 6.131A pdb=" N VAL H 147 " --> pdb=" O GLU H 246 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 162 through 163 460 hydrogen bonds defined for protein. 1284 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1559 1.33 - 1.45: 2236 1.45 - 1.57: 4728 1.57 - 1.69: 0 1.69 - 1.82: 68 Bond restraints: 8591 Sorted by residual: bond pdb=" C PRO G 60 " pdb=" O PRO G 60 " ideal model delta sigma weight residual 1.239 1.204 0.035 1.22e-02 6.72e+03 8.11e+00 bond pdb=" N ARG A 231 " pdb=" CA ARG A 231 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.30e-02 5.92e+03 7.11e+00 bond pdb=" N VAL C 388 " pdb=" CA VAL C 388 " ideal model delta sigma weight residual 1.461 1.491 -0.029 1.17e-02 7.31e+03 6.31e+00 bond pdb=" N GLU A 330 " pdb=" CA GLU A 330 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.25e-02 6.40e+03 5.81e+00 bond pdb=" CA PHE A 208 " pdb=" CB PHE A 208 " ideal model delta sigma weight residual 1.526 1.565 -0.039 1.68e-02 3.54e+03 5.34e+00 ... (remaining 8586 not shown) Histogram of bond angle deviations from ideal: 98.32 - 105.47: 171 105.47 - 112.61: 4430 112.61 - 119.76: 2892 119.76 - 126.90: 4081 126.90 - 134.04: 123 Bond angle restraints: 11697 Sorted by residual: angle pdb=" C PHE A 273 " pdb=" N LYS A 274 " pdb=" CA LYS A 274 " ideal model delta sigma weight residual 120.44 115.14 5.30 1.30e+00 5.92e-01 1.66e+01 angle pdb=" N ASP A 272 " pdb=" CA ASP A 272 " pdb=" C ASP A 272 " ideal model delta sigma weight residual 111.07 107.05 4.02 1.07e+00 8.73e-01 1.41e+01 angle pdb=" N LYS A 274 " pdb=" CA LYS A 274 " pdb=" C LYS A 274 " ideal model delta sigma weight residual 111.07 107.10 3.97 1.07e+00 8.73e-01 1.37e+01 angle pdb=" N GLU A 21 " pdb=" CA GLU A 21 " pdb=" C GLU A 21 " ideal model delta sigma weight residual 111.07 107.25 3.82 1.07e+00 8.73e-01 1.27e+01 angle pdb=" N PRO C 156 " pdb=" CA PRO C 156 " pdb=" C PRO C 156 " ideal model delta sigma weight residual 113.78 108.15 5.63 1.62e+00 3.81e-01 1.21e+01 ... (remaining 11692 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4598 17.97 - 35.94: 352 35.94 - 53.90: 62 53.90 - 71.87: 20 71.87 - 89.84: 6 Dihedral angle restraints: 5038 sinusoidal: 1773 harmonic: 3265 Sorted by residual: dihedral pdb=" CA ASN A 279 " pdb=" C ASN A 279 " pdb=" N ARG A 280 " pdb=" CA ARG A 280 " ideal model delta harmonic sigma weight residual 180.00 -152.35 -27.65 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA PRO G 53 " pdb=" C PRO G 53 " pdb=" N VAL G 54 " pdb=" CA VAL G 54 " ideal model delta harmonic sigma weight residual 180.00 -158.45 -21.55 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA THR B 165 " pdb=" C THR B 165 " pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta harmonic sigma weight residual 180.00 160.39 19.61 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 5035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1188 0.071 - 0.142: 155 0.142 - 0.213: 6 0.213 - 0.284: 0 0.284 - 0.355: 1 Chirality restraints: 1350 Sorted by residual: chirality pdb=" CA ASN B 313 " pdb=" N ASN B 313 " pdb=" C ASN B 313 " pdb=" CB ASN B 313 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CB VAL C 388 " pdb=" CA VAL C 388 " pdb=" CG1 VAL C 388 " pdb=" CG2 VAL C 388 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ARG A 333 " pdb=" N ARG A 333 " pdb=" C ARG A 333 " pdb=" CB ARG A 333 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.63e-01 ... (remaining 1347 not shown) Planarity restraints: 1495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 325 " 0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO A 326 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 326 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 326 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 340 " 0.010 2.00e-02 2.50e+03 1.21e-02 2.56e+00 pdb=" CG PHE A 340 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 340 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 340 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 340 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 340 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 340 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 347 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO C 348 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 348 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 348 " -0.022 5.00e-02 4.00e+02 ... (remaining 1492 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 41 2.55 - 3.14: 7128 3.14 - 3.72: 13063 3.72 - 4.31: 18059 4.31 - 4.90: 30403 Nonbonded interactions: 68694 Sorted by model distance: nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 1.959 2.440 nonbonded pdb=" N GLU G 47 " pdb=" OE1 GLU G 47 " model vdw 2.100 2.520 nonbonded pdb=" O MET C 138 " pdb=" OG SER C 141 " model vdw 2.246 2.440 nonbonded pdb=" NH1 ARG C 340 " pdb=" OXT ARG D 10 " model vdw 2.290 2.520 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.302 2.440 ... (remaining 68689 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.330 Check model and map are aligned: 0.140 Set scattering table: 0.070 Process input model: 27.180 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8591 Z= 0.259 Angle : 0.758 8.005 11697 Z= 0.443 Chirality : 0.046 0.355 1350 Planarity : 0.005 0.052 1495 Dihedral : 14.154 89.840 2917 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.19 % Allowed : 12.53 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.26), residues: 1103 helix: 0.57 (0.25), residues: 390 sheet: -0.38 (0.30), residues: 293 loop : -0.24 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.006 0.002 HIS H 167 PHE 0.028 0.002 PHE A 340 TYR 0.016 0.002 TYR C 393 ARG 0.007 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 205 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.6924 (mmm) cc_final: 0.6705 (mpp) REVERT: A 274 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.9039 (mttp) REVERT: A 391 TYR cc_start: 0.6059 (OUTLIER) cc_final: 0.5514 (m-80) REVERT: B 67 SER cc_start: 0.8448 (t) cc_final: 0.7879 (t) REVERT: H 184 SER cc_start: 0.9289 (p) cc_final: 0.8987 (m) REVERT: D 6 MET cc_start: 0.8072 (tpp) cc_final: 0.7682 (tpp) outliers start: 10 outliers final: 2 residues processed: 212 average time/residue: 0.2315 time to fit residues: 64.3282 Evaluate side-chains 177 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 173 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 434 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.4980 chunk 99 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 278 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8591 Z= 0.228 Angle : 0.627 7.223 11697 Z= 0.331 Chirality : 0.044 0.151 1350 Planarity : 0.004 0.052 1495 Dihedral : 5.978 57.103 1217 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.74 % Allowed : 12.65 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.26), residues: 1103 helix: 1.51 (0.26), residues: 394 sheet: -0.20 (0.30), residues: 285 loop : -0.09 (0.33), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 297 HIS 0.006 0.001 HIS C 394 PHE 0.025 0.002 PHE A 208 TYR 0.014 0.002 TYR A 318 ARG 0.005 0.001 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 198 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 212 PHE cc_start: 0.8128 (p90) cc_final: 0.7792 (p90) REVERT: A 295 ASP cc_start: 0.8849 (p0) cc_final: 0.8428 (p0) REVERT: B 49 ARG cc_start: 0.6829 (mmm160) cc_final: 0.6623 (mmt180) REVERT: B 234 PHE cc_start: 0.8648 (OUTLIER) cc_final: 0.7784 (m-80) REVERT: H 184 SER cc_start: 0.9330 (p) cc_final: 0.9078 (m) REVERT: C 34 PHE cc_start: 0.8583 (t80) cc_final: 0.8295 (t80) REVERT: C 92 ARG cc_start: 0.7056 (tpt-90) cc_final: 0.5849 (tmm-80) REVERT: C 160 TYR cc_start: 0.6763 (t80) cc_final: 0.6389 (t80) REVERT: C 355 CYS cc_start: 0.8413 (m) cc_final: 0.7934 (m) REVERT: C 418 HIS cc_start: 0.7516 (m90) cc_final: 0.7283 (m90) outliers start: 23 outliers final: 16 residues processed: 212 average time/residue: 0.2130 time to fit residues: 60.6730 Evaluate side-chains 193 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 176 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain H residue 1 ASP Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 174 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.0770 chunk 31 optimal weight: 0.0370 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 overall best weight: 0.5816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 167 HIS H 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8591 Z= 0.197 Angle : 0.591 7.358 11697 Z= 0.308 Chirality : 0.043 0.147 1350 Planarity : 0.004 0.045 1495 Dihedral : 5.090 55.243 1211 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.10 % Allowed : 15.27 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.26), residues: 1103 helix: 1.67 (0.26), residues: 402 sheet: -0.12 (0.30), residues: 275 loop : -0.02 (0.33), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 63 HIS 0.007 0.001 HIS C 394 PHE 0.032 0.002 PHE A 208 TYR 0.013 0.001 TYR A 318 ARG 0.005 0.001 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 189 time to evaluate : 0.996 Fit side-chains REVERT: A 295 ASP cc_start: 0.8909 (p0) cc_final: 0.8601 (p0) REVERT: B 168 LEU cc_start: 0.8779 (tp) cc_final: 0.8351 (tt) REVERT: B 234 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.7626 (m-80) REVERT: B 292 PHE cc_start: 0.8653 (m-10) cc_final: 0.8365 (m-80) REVERT: H 184 SER cc_start: 0.9428 (p) cc_final: 0.9151 (m) REVERT: C 92 ARG cc_start: 0.7027 (tpt-90) cc_final: 0.5812 (tmm-80) REVERT: C 107 PHE cc_start: 0.6257 (m-80) cc_final: 0.5994 (m-80) REVERT: C 160 TYR cc_start: 0.6771 (t80) cc_final: 0.6298 (t80) REVERT: C 355 CYS cc_start: 0.8458 (m) cc_final: 0.8013 (m) REVERT: C 414 MET cc_start: 0.7749 (ppp) cc_final: 0.7542 (ppp) REVERT: C 418 HIS cc_start: 0.7451 (m90) cc_final: 0.7124 (m90) REVERT: D 6 MET cc_start: 0.8226 (tpp) cc_final: 0.7920 (tpp) outliers start: 26 outliers final: 19 residues processed: 201 average time/residue: 0.2224 time to fit residues: 61.5799 Evaluate side-chains 186 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 166 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain H residue 1 ASP Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 412 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 20.0000 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 100 optimal weight: 0.0970 chunk 106 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 28 optimal weight: 0.4980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 183 GLN ** C 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8591 Z= 0.181 Angle : 0.565 6.559 11697 Z= 0.294 Chirality : 0.043 0.193 1350 Planarity : 0.004 0.048 1495 Dihedral : 4.876 55.754 1211 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.30 % Allowed : 14.80 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.26), residues: 1103 helix: 1.75 (0.26), residues: 407 sheet: -0.12 (0.30), residues: 282 loop : 0.01 (0.33), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 88 HIS 0.008 0.001 HIS C 394 PHE 0.025 0.002 PHE A 340 TYR 0.014 0.001 TYR A 318 ARG 0.003 0.000 ARG C 340 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 187 time to evaluate : 0.884 Fit side-chains REVERT: A 295 ASP cc_start: 0.8897 (p0) cc_final: 0.8394 (p0) REVERT: A 385 GLN cc_start: 0.8007 (mt0) cc_final: 0.7664 (mt0) REVERT: B 168 LEU cc_start: 0.8766 (tp) cc_final: 0.8354 (tt) REVERT: B 198 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7553 (pp) REVERT: B 234 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.7634 (m-80) REVERT: B 292 PHE cc_start: 0.8610 (m-10) cc_final: 0.8263 (m-10) REVERT: H 184 SER cc_start: 0.9438 (p) cc_final: 0.9090 (m) REVERT: C 92 ARG cc_start: 0.6907 (tpt-90) cc_final: 0.5730 (tmm-80) REVERT: C 355 CYS cc_start: 0.8489 (m) cc_final: 0.8070 (m) REVERT: C 418 HIS cc_start: 0.7445 (m90) cc_final: 0.7223 (m90) REVERT: D 6 MET cc_start: 0.8320 (tpp) cc_final: 0.7934 (tpp) outliers start: 36 outliers final: 20 residues processed: 207 average time/residue: 0.1970 time to fit residues: 56.3256 Evaluate side-chains 198 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 176 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain H residue 1 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 353 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 43 optimal weight: 0.0060 chunk 90 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 26 optimal weight: 0.1980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 183 GLN ** C 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8591 Z= 0.180 Angle : 0.564 6.656 11697 Z= 0.293 Chirality : 0.042 0.157 1350 Planarity : 0.004 0.049 1495 Dihedral : 4.594 56.378 1209 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.53 % Allowed : 15.75 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.26), residues: 1103 helix: 1.81 (0.26), residues: 407 sheet: -0.18 (0.30), residues: 281 loop : -0.15 (0.33), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 88 HIS 0.004 0.001 HIS H 35 PHE 0.016 0.001 PHE C 151 TYR 0.014 0.001 TYR A 318 ARG 0.003 0.000 ARG D 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 189 time to evaluate : 1.025 Fit side-chains REVERT: A 205 SER cc_start: 0.8774 (t) cc_final: 0.8432 (p) REVERT: A 295 ASP cc_start: 0.8873 (p0) cc_final: 0.8561 (p0) REVERT: B 13 GLN cc_start: 0.8868 (pp30) cc_final: 0.8523 (pp30) REVERT: B 168 LEU cc_start: 0.8809 (tp) cc_final: 0.8395 (tt) REVERT: B 198 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7588 (pp) REVERT: B 215 GLU cc_start: 0.6691 (tm-30) cc_final: 0.6370 (tm-30) REVERT: B 234 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.7680 (m-80) REVERT: B 292 PHE cc_start: 0.8523 (m-10) cc_final: 0.8215 (m-10) REVERT: H 184 SER cc_start: 0.9424 (p) cc_final: 0.9033 (m) REVERT: C 355 CYS cc_start: 0.8469 (m) cc_final: 0.8050 (m) REVERT: C 418 HIS cc_start: 0.7446 (m90) cc_final: 0.7208 (m90) outliers start: 38 outliers final: 25 residues processed: 212 average time/residue: 0.1923 time to fit residues: 56.7904 Evaluate side-chains 199 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 172 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 1 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 353 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.0070 chunk 95 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 55 optimal weight: 8.9990 chunk 102 optimal weight: 0.4980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 GLN C 131 GLN ** C 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8591 Z= 0.185 Angle : 0.601 10.913 11697 Z= 0.305 Chirality : 0.043 0.258 1350 Planarity : 0.004 0.048 1495 Dihedral : 4.517 55.890 1209 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.30 % Allowed : 17.54 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.26), residues: 1103 helix: 1.80 (0.26), residues: 408 sheet: -0.22 (0.30), residues: 279 loop : -0.12 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 88 HIS 0.007 0.001 HIS C 394 PHE 0.019 0.001 PHE A 340 TYR 0.012 0.001 TYR B 111 ARG 0.004 0.000 ARG H 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 185 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: A 205 SER cc_start: 0.8765 (t) cc_final: 0.8406 (p) REVERT: A 218 ASN cc_start: 0.8325 (p0) cc_final: 0.8063 (p0) REVERT: A 295 ASP cc_start: 0.8859 (p0) cc_final: 0.8500 (p0) REVERT: B 168 LEU cc_start: 0.8796 (tp) cc_final: 0.8373 (tt) REVERT: B 198 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7560 (pp) REVERT: B 215 GLU cc_start: 0.6698 (tm-30) cc_final: 0.6363 (tt0) REVERT: B 234 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.7658 (m-80) REVERT: B 292 PHE cc_start: 0.8536 (m-10) cc_final: 0.8238 (m-10) REVERT: H 184 SER cc_start: 0.9426 (p) cc_final: 0.9020 (m) REVERT: H 231 GLN cc_start: 0.8316 (pp30) cc_final: 0.7804 (pp30) REVERT: C 355 CYS cc_start: 0.8456 (m) cc_final: 0.8042 (m) REVERT: C 413 LEU cc_start: 0.8806 (mm) cc_final: 0.8276 (tp) REVERT: C 418 HIS cc_start: 0.7510 (m90) cc_final: 0.7261 (m90) REVERT: D 6 MET cc_start: 0.8264 (tpp) cc_final: 0.7880 (tpp) outliers start: 36 outliers final: 25 residues processed: 201 average time/residue: 0.1930 time to fit residues: 54.1113 Evaluate side-chains 208 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 181 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 1 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 373 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.0040 chunk 60 optimal weight: 0.2980 chunk 77 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 GLN ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8591 Z= 0.202 Angle : 0.598 9.116 11697 Z= 0.307 Chirality : 0.043 0.280 1350 Planarity : 0.004 0.049 1495 Dihedral : 4.536 55.586 1209 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.18 % Allowed : 17.30 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.26), residues: 1103 helix: 1.83 (0.26), residues: 405 sheet: -0.26 (0.30), residues: 279 loop : -0.10 (0.33), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 47 HIS 0.003 0.001 HIS B 225 PHE 0.025 0.002 PHE A 208 TYR 0.014 0.001 TYR A 318 ARG 0.004 0.000 ARG H 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 183 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 SER cc_start: 0.8768 (t) cc_final: 0.8411 (p) REVERT: A 218 ASN cc_start: 0.8320 (p0) cc_final: 0.8024 (p0) REVERT: A 295 ASP cc_start: 0.8846 (p0) cc_final: 0.8510 (p0) REVERT: B 168 LEU cc_start: 0.8830 (tp) cc_final: 0.8402 (tt) REVERT: B 198 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7592 (pp) REVERT: B 215 GLU cc_start: 0.6808 (tm-30) cc_final: 0.6483 (tt0) REVERT: B 234 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.7687 (m-80) REVERT: B 292 PHE cc_start: 0.8523 (m-10) cc_final: 0.8206 (m-10) REVERT: G 42 GLU cc_start: 0.8066 (tp30) cc_final: 0.7747 (tm-30) REVERT: H 184 SER cc_start: 0.9417 (p) cc_final: 0.8978 (m) REVERT: H 231 GLN cc_start: 0.8302 (pp30) cc_final: 0.7768 (pp30) REVERT: C 355 CYS cc_start: 0.8474 (m) cc_final: 0.8059 (m) REVERT: C 413 LEU cc_start: 0.8763 (mm) cc_final: 0.8313 (tp) REVERT: C 418 HIS cc_start: 0.7475 (m90) cc_final: 0.7230 (m90) REVERT: D 6 MET cc_start: 0.8394 (tpp) cc_final: 0.7912 (tpp) outliers start: 35 outliers final: 27 residues processed: 201 average time/residue: 0.1918 time to fit residues: 54.0973 Evaluate side-chains 207 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 178 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 1 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 399 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 67 optimal weight: 0.4980 chunk 72 optimal weight: 0.0370 chunk 52 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 GLN ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8591 Z= 0.188 Angle : 0.608 11.021 11697 Z= 0.307 Chirality : 0.043 0.273 1350 Planarity : 0.004 0.049 1495 Dihedral : 4.468 55.677 1209 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.22 % Allowed : 18.97 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.26), residues: 1103 helix: 1.96 (0.26), residues: 402 sheet: -0.34 (0.30), residues: 271 loop : -0.05 (0.33), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP H 47 HIS 0.004 0.001 HIS A 357 PHE 0.024 0.001 PHE A 208 TYR 0.016 0.001 TYR C 160 ARG 0.005 0.000 ARG H 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 189 time to evaluate : 0.975 Fit side-chains REVERT: A 205 SER cc_start: 0.8766 (t) cc_final: 0.8385 (p) REVERT: A 218 ASN cc_start: 0.8320 (p0) cc_final: 0.8022 (p0) REVERT: A 295 ASP cc_start: 0.8808 (p0) cc_final: 0.8500 (p0) REVERT: B 168 LEU cc_start: 0.8815 (tp) cc_final: 0.8373 (tt) REVERT: B 198 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7615 (pp) REVERT: B 215 GLU cc_start: 0.6744 (tm-30) cc_final: 0.6394 (tt0) REVERT: B 234 PHE cc_start: 0.8592 (OUTLIER) cc_final: 0.7625 (m-80) REVERT: B 292 PHE cc_start: 0.8464 (m-10) cc_final: 0.8183 (m-10) REVERT: H 184 SER cc_start: 0.9450 (p) cc_final: 0.8932 (m) REVERT: H 231 GLN cc_start: 0.8218 (pp30) cc_final: 0.7651 (pp30) REVERT: C 355 CYS cc_start: 0.8465 (m) cc_final: 0.8054 (m) REVERT: C 413 LEU cc_start: 0.8775 (mm) cc_final: 0.8337 (tp) REVERT: C 418 HIS cc_start: 0.7475 (m90) cc_final: 0.7225 (m90) REVERT: D 6 MET cc_start: 0.8305 (tpp) cc_final: 0.7759 (tpp) outliers start: 27 outliers final: 24 residues processed: 202 average time/residue: 0.1946 time to fit residues: 54.3248 Evaluate side-chains 208 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 182 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 1 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 399 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 9.9990 chunk 101 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 30 optimal weight: 0.0570 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 64 optimal weight: 0.1980 chunk 104 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 GLN ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8591 Z= 0.191 Angle : 0.618 11.153 11697 Z= 0.318 Chirality : 0.043 0.294 1350 Planarity : 0.004 0.045 1495 Dihedral : 4.425 54.087 1209 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.34 % Allowed : 19.81 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.26), residues: 1103 helix: 1.93 (0.26), residues: 402 sheet: -0.18 (0.32), residues: 261 loop : -0.08 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP H 47 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.001 PHE A 340 TYR 0.014 0.001 TYR B 111 ARG 0.005 0.000 ARG H 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 195 time to evaluate : 0.987 Fit side-chains REVERT: A 205 SER cc_start: 0.8764 (t) cc_final: 0.8384 (p) REVERT: A 218 ASN cc_start: 0.8319 (p0) cc_final: 0.8033 (p0) REVERT: A 295 ASP cc_start: 0.8775 (p0) cc_final: 0.8516 (p0) REVERT: B 168 LEU cc_start: 0.8885 (tp) cc_final: 0.8445 (tt) REVERT: B 198 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7695 (pp) REVERT: B 215 GLU cc_start: 0.6743 (tm-30) cc_final: 0.6385 (tt0) REVERT: B 234 PHE cc_start: 0.8596 (OUTLIER) cc_final: 0.7610 (m-80) REVERT: B 292 PHE cc_start: 0.8425 (m-10) cc_final: 0.8153 (m-10) REVERT: H 184 SER cc_start: 0.9460 (p) cc_final: 0.8918 (m) REVERT: H 231 GLN cc_start: 0.8169 (pp30) cc_final: 0.7789 (pp30) REVERT: C 355 CYS cc_start: 0.8422 (m) cc_final: 0.8004 (m) REVERT: C 413 LEU cc_start: 0.8729 (mm) cc_final: 0.8301 (tp) REVERT: D 6 MET cc_start: 0.8369 (tpp) cc_final: 0.7849 (tpp) outliers start: 28 outliers final: 26 residues processed: 209 average time/residue: 0.2063 time to fit residues: 58.8779 Evaluate side-chains 210 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 182 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 1 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 399 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.5980 chunk 72 optimal weight: 0.0980 chunk 109 optimal weight: 7.9990 chunk 100 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 9 optimal weight: 0.0670 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 26 optimal weight: 0.0670 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 GLN ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8591 Z= 0.168 Angle : 0.618 11.848 11697 Z= 0.310 Chirality : 0.042 0.279 1350 Planarity : 0.004 0.045 1495 Dihedral : 4.358 54.859 1209 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.51 % Allowed : 21.12 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.26), residues: 1103 helix: 1.94 (0.26), residues: 402 sheet: -0.18 (0.32), residues: 259 loop : -0.04 (0.32), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 47 HIS 0.004 0.001 HIS H 35 PHE 0.019 0.001 PHE A 208 TYR 0.018 0.001 TYR C 160 ARG 0.008 0.001 ARG B 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 185 time to evaluate : 1.000 Fit side-chains REVERT: A 205 SER cc_start: 0.8744 (t) cc_final: 0.8364 (p) REVERT: A 218 ASN cc_start: 0.8315 (p0) cc_final: 0.8029 (p0) REVERT: A 295 ASP cc_start: 0.8726 (p0) cc_final: 0.8507 (p0) REVERT: B 168 LEU cc_start: 0.8895 (tp) cc_final: 0.8470 (tt) REVERT: B 198 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7760 (pp) REVERT: B 215 GLU cc_start: 0.6665 (tm-30) cc_final: 0.6284 (tt0) REVERT: B 234 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.7622 (m-80) REVERT: B 327 VAL cc_start: 0.8844 (OUTLIER) cc_final: 0.8606 (m) REVERT: H 180 ARG cc_start: 0.7866 (mtm-85) cc_final: 0.6898 (mtt90) REVERT: H 184 SER cc_start: 0.9451 (p) cc_final: 0.8906 (m) REVERT: H 231 GLN cc_start: 0.8084 (pp30) cc_final: 0.7721 (pp30) REVERT: C 355 CYS cc_start: 0.8370 (m) cc_final: 0.7943 (m) REVERT: C 413 LEU cc_start: 0.8730 (mm) cc_final: 0.8322 (tp) REVERT: D 6 MET cc_start: 0.8325 (tpp) cc_final: 0.7783 (tpp) outliers start: 21 outliers final: 17 residues processed: 196 average time/residue: 0.2020 time to fit residues: 54.3947 Evaluate side-chains 199 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 179 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 1 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 399 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.0870 chunk 76 optimal weight: 0.0870 chunk 4 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 GLN ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.191660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.149364 restraints weight = 10766.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.149246 restraints weight = 6140.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.150974 restraints weight = 5202.096| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8591 Z= 0.189 Angle : 0.616 11.643 11697 Z= 0.314 Chirality : 0.043 0.273 1350 Planarity : 0.004 0.048 1495 Dihedral : 4.397 54.683 1209 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.74 % Allowed : 21.12 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.26), residues: 1103 helix: 1.96 (0.26), residues: 402 sheet: -0.17 (0.32), residues: 255 loop : -0.04 (0.32), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 88 HIS 0.004 0.001 HIS C 394 PHE 0.026 0.001 PHE A 208 TYR 0.014 0.001 TYR B 111 ARG 0.008 0.001 ARG B 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2095.52 seconds wall clock time: 38 minutes 50.40 seconds (2330.40 seconds total)